From c69906668b9fa0cfafc50ec28a6730824e66058f Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 28 Nov 2017 13:24:30 -0500
Subject: [PATCH] implement Class1AffinityPredictor.merge() method
---
.../class1_affinity_predictor.py | 59 ++++++++++++++++++-
1 file changed, 58 insertions(+), 1 deletion(-)
diff --git a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py b/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
index b424aaf5..fa0623fb 100644
--- a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
@@ -96,10 +96,67 @@ class Class1AffinityPredictor(object):
columns=["model_name", "allele", "config_json", "model"])
self.manifest_df = manifest_df
- if allele_to_percent_rank_transform is None:
+ if not allele_to_percent_rank_transform:
allele_to_percent_rank_transform = {}
self.allele_to_percent_rank_transform = allele_to_percent_rank_transform
+ @property
+ def neural_networks(self):
+ """
+ List of the neural networks in the ensemble.
+
+ Returns
+ -------
+ list of Class1NeuralNetwork
+ """
+ result = []
+ for models in self.allele_to_allele_specific_models.values():
+ result.extend(models)
+ result.extend(self.class1_pan_allele_models)
+ return result
+
+ @classmethod
+ def merge(cls, predictors):
+ """
+ Merge the ensembles of two or more Class1AffinityPredictor instances.
+
+ Note: the resulting merged predictor will NOT have calibrated percentile
+ ranks. Call calibrate_percentile_ranks() on it if these are needed.
+
+ Parameters
+ ----------
+ predictors : sequence of Class1AffinityPredictor
+
+ Returns
+ -------
+ Class1AffinityPredictor
+
+ """
+ assert len(predictors) > 0
+ if len(predictors) == 1:
+ return predictors[0]
+
+ allele_to_allele_specific_models = collections.defaultdict(list)
+ class1_pan_allele_models = []
+ allele_to_pseudosequence = predictors[0].allele_to_pseudosequence
+
+ for predictor in predictors:
+ for (allele, networks) in (
+ predictor.allele_to_allele_specific_models.items()):
+ allele_to_allele_specific_models[allele].extend(networks)
+ class1_pan_allele_models.extend(
+ predictor.class1_pan_allele_models)
+
+ return Class1AffinityPredictor(
+ allele_to_allele_specific_models=allele_to_allele_specific_models,
+ class1_pan_allele_models=class1_pan_allele_models,
+ allele_to_pseudosequence=allele_to_pseudosequence
+ )
+
+ @property
+ def num_networks(self):
+ return self.manifest_df.shape[0]
+
@property
def supported_alleles(self):
--
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